MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. To build ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file.

Inputs:

• a file containing the sequences to analyse in fasta format
• psi-blast parameters. Default will be -j 10 -e 0.01 -h 0.01. If you want to change something please enter INTER= value to change -j option, E_EXPECT=value for -e option and H_EXPECT=value for -h option.

Outputs:

the log file

the alignment file of the sequences in srs format

the results of the analysis in xdom format

the project file used to launch xdom faster

A perl script is available here to run this webservice from your computer. Please install SOAP Lite before.

Name

MkDom2

Documentation

http://prodom.prabi.fr/prodom/current/documentation/mkdom2.html

Protocol

SOAP

WSDL

Endpoint

http://prodom.prabi.fr/prodom/2006.1/cgi-bin/essaimkdom.cgi

Topic

Domains

Type

Analysis

Tags

Clustering, EMBRACE, INRIA-UCBL, ProDom, protein domain prediction, protein sequence

Description

MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that [...]

Further information

MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. To build ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file.

Inputs:

• a file containing the sequences to analyse in fasta format
• psi-blast parameters. Default will be -j 10 -e 0.01 -h 0.01. If you want to change something please enter INTER= value to change -j option, E_EXPECT=value for -e option and H_EXPECT=value for -h option.

Outputs:

the log file

the alignment file of the sequences in srs format

the results of the analysis in xdom format

the project file used to launch xdom faster

A perl script is available here to run this webservice from your computer. Please install SOAP Lite before.

Original source

BioCatalogue

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